Finding Mr Right
by DorothyOz
Summary: After his time with Chaya, John starts to think about the man he loves. This story was written for the 2015 Secret Santa for icarusancalion. I hope you like it.


**Finding Mr. Right**

* * *

 **A/N: please read**

 **Title:** Finding Mr. Right

 **Recipient:** icarusancalion

 **Summary:** After his time with Chaya, John starts to think about the man he loves.

 **Genre:** Romance, friendship, Atlantis politics

 **Season/episode:** SG: Atlantis, season 1

 **Spoilers:** Stargate movie, Stargate: SG1 (all seasons and movies), and SG: Atlantis (season 1)

 **Pairing:** John Sheppard/OMC (more like imagine whoever you want as John's boyfriend).

 **Rating:** T

 **Warnings:** No warnings

 **Disclaimer:** Read profile

 **Acknowledgments:** Big thanks to **Amycat8733** for beta-reading this story for me.

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This story was written for the **2015 Secret Santa** for **icarusancalion**. I hope you like it.

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 **Finding Mr. Right**

* * *

After leaving Chaya's planet, John felt the need for solitude and he went looking for it on one of the more secluded balconies of the city. The mind meld had forced him to stop thinking only about survival and focus on himself, even if only for a few minutes. It had been a very long time since he had felt attracted to anyone and even more since he had been in love. Chaya had made him think about that time, about the man he still loved, about how he met him.

* * *

John was acing flight school so when they had a couple of days off, he decided to enjoy them. He went to a little, discrete, gay bar he had found recently. It was a calm place where people went for burgers, beers, and pool. It wasn't one of those big dancing places or an obviously gay bar in the gay neighborhood of the city. He was terrified of going to one of those places and getting caught. He loved flying and he wasn't willing to lose it for anything, let alone a night of dancing. This place was the most straight-looking gay pool bar he had ever seen, which benefitted him because it helped him keep his anonymity.

He was enjoying a beer and the newspaper when a young, blonde, blue-eyed guy he recognized from school entered the establishment and drew his attention. He had seen him fly and he was very good; he was also kind and until this moment he had thought, straight. Straight, popular, and gorgeous flyboy who would have never paid any attention to the lanky nerd Sheppard saw in himself, no matter how big his crush on him was.

Terrified as John was at being caught, he hid behind his newspaper only to be interrupted a few minutes later. The gorgeous man sat in front of him, at the other side of the table, with a beer in his hand. He was smiling at him warmly.

"I'm not going to rat you out, John. Can I call you John? I'm here for the same reason you are. You're not going to rat me out either, right?"

"Yes. No. Sorry. Yes, you may call me John. No, I won't rat you out." John was so nervous he was rambling. He knew it, he just couldn't stop it.

Gorgeous smiled at him again and they started talking. Somehow they ended talking until the bar closed, and John went to bed smiling like an idiot.

After that night, they started hanging out constantly under the disguise of studying, running or training together. For the outside world, they were friends and colleagues, appearing to some as the nerd helping the popular kid with his math. They weren't wrong, but it wasn't the only thing between them. They were getting closer with every day they spent together, to the point it was getting increasingly difficult for John to deny that they were dating. It really wasn't helping John with his ever growing crush on the man, who couldn't possibly feel the same.

Or so John believed until one day when they were studying physics in John's room when everything changed. John was explaining something and Gorgeous was looking at him with an amazed expression. Without warning he kissed John. He was stunned and froze afraid to move or breathe and having his friend stop.

Gorgeous stopped, believing he had scared John or had done something wrong. "What's wrong? You don't want this?"

"Yeah, I do, I want it. I didn't think you…"

John couldn't finish his sentence. "I want to. You have no idea how hot you are when you talk geek! I'm crazy about you, John."

John had never had anyone be attracted to his brain, and now this man thought it was hot. He kissed him back leaving his doubts and insecurities behind.

* * *

Sheppard couldn't stop himself from smiling remembering that day. It was the first time he slept with a guy. They made love all night long, and John had never felt so loved in his life.

They dated for months, the happiest of John's life. When he had merged his mind with Chaya, she had showed him the people of her planet wanting to make him understand her decision to protect them. John had let her see pieces of this time and now with his mind open to the memories he couldn't stop them. The memory of the happiness and love they shared, his smile, the way he kissed him…

He was smiling like an idiot when McKay found him in the balcony.

* * *

Rodney knew he had been too hard on Sheppard about the Ancient Priestess and her crush on him. He knew he had judged him too harshly. He should apologize and repair their friendship before it went to hell, like most of his past friendships. However, he didn't know how to do it because the Major was extremely angry and he had excuses but no explanations. If he was honest, and he didn't want to be honest, he had been jealous of Sheppard because he got to be Kirk and he didn't.

As much as he dreaded it, Rodney went looking for Sheppard to repair their friendship and he found him on one of the empty balconies alone. The Major was smiling at himself and Rodney groaned, thinking he was probably thinking about the Ancient chick.

"Something you want, McKay?" John asked without looking at the scientist.

"I wanted to say that I may have overreacted, you know about Chaya..."

"You may have?" Sheppard repeated filling his voice with the anger he felt at that moment.

"Ok. I did it. I'm sorry," McKay admitted. John nodded accepting the apology but made no move to welcome Rodney into his refuge. "Well, I'll go and let you think about the hot alien chick."

"I'm not thinking about her."

"You're not? Because you were smiling in a very stupid way. Love struck, I'd dare say."

"I was not."

"You were." They were looking at each other trying to read the other. In the few months they've been in Pegasus they have gotten closer, and while none of them would describe the other as a close friend, they would call each other friends. They may have been angry at each other, but they wanted to keep that friendship.

The staring contest ended when John smirked and made the tiniest gesture with his head inviting Rodney to join him in the balcony. "I really wasn't thinking about Chaya."

"You weren't? Then who?"

"Someone I knew, back on Earth."

"You have a girlfriend back on Earth? Is she hot?"

"McKay!" Rodney looked shamed at the reprimand and so John answered. "No, I don't have a girlfriend on Earth. When I was in flight school, I met someone, we fell in love…"

"So wife?"

"No. We were together for years and then I got scared and screwed it up. I broke it off. Worst decision of my life, I tell you, followed only by getting married to Nancy, a woman my father approved of. That should have been warning enough, but it wasn't. I loved Nancy but not the same way. We didn't work. She couldn't deal with my career, the secrets…"

"Got divorced?"

"Yep. After a while, I met my friend from flight school again. Somehow we started dating again, we're happy. Then..." John went silent and his face shadowed with the sad memories.

"Then what?"

"He got into some kind of secret program to test secret fighter jets. I was okay with the secrets; I could deal with the extra danger. Sure I wanted to test secret cool fighter jets too, but I was happy with flying choppers. I loved it! Still miss it every day."

"Ok, so your flygirl got into flying crazy ass secret fighter planes. What's the problem? Well, aside from the very obvious one of you being in Pegasus without any possible way home and the impending threat of death due to the Wraith… and who knows what else…"

John ignored the confusion about the gender of his partner and Rodney's ramblings. "He disappeared one day. Just vanished. No one knew, of course, so no one knew to notify me so he could have been killed or something. He wasn't listed as dead though, so after a while with no contact, I just accepted that things weren't as good as I thought they were…"

"Wait, wait, wait. Give me a second to process all this. You said HE?"

"Shush, McKay!"

"Sorry. You said HE?" Rodney asked again in a low voice.

"Yeah."

"Okay." Rodney nodded reassuringly hoping to show the Major that he had no problem with his revelation, that he appreciated his confession, and would keep his secret safe. "He went into some secret program testing cool fighter planes? Was this program in Colorado?"

"Yeah. You think he was in the SGC?"

"If he was a fighter pilot, probably he went into the 302 program." Rodney's mind started to work trying to figure out what could have happened to his friend's lover. "He could have been in the battle of Antarctica against Anubis' forces. If he was injured, he would have been sent to the Academy Hospital and his family would have been notified."

"Not me. No one knew about us. No one at all."

"Not even his family or a friend?"

"No one, Rodney."

"We don't have a list of personnel involved in the 302 program or even the SGC, but we have lots of reports, we could check them out to see if we can track him down."

"Thanks, Rodney, but I don't think it's worth the effort. First, we're very far away from Earth to matter. Second, and more important, he just gave up on me. We had been arguing a lot, mostly about telling his folks and some friends. I didn't want out and he did. I'm not good at expressing feelings. He was getting tired of my shit, I could tell. He just got enough."

"Without even saying 'so long'? You sure?"

John nodded sadly. He had been the only person to show him love, to love him for who he was and not who they wanted him to be, but ultimately he wasn't enough. It was the only explanation. Also, the alternative was that he had been killed or injured severely and had been unable to contact him for the five months that had passed since his disappearance and the departure of the Expedition. John refused to contemplate that option, he still loved him too much.

"If you're right, you should stop pining for that jerk. You'll find someone else, nicer, preferably someone who's not an ascended ancient anchored to one planet for all eternity."

"Thanks, Rodney."

They sat in comfortable silence for a bit before the next emergency forced them back into the center of operations of the city.

* * *

Rodney knew he had been entrusted with Sheppard's biggest secret and he should probably leave it alone. However, Sheppard had looked extremely depressed at the possibility of his lover abandoning him or maybe the chance, that John obviously didn't want to contemplate, that he was killed in action or was injured to the point of being unable to contact him.

The scientist decided to investigate a little, maybe he could find an explanation. Elizabeth had been in charge of the SGC for a brief period of time during Anubis' attempt to invade Earth, she may have the information he needed. Rodney went over every report pertaining to that time looking for male USAF fighter pilots involved in the battle. He managed to get a very long list of USAF male pilots from the SGC and the Prometheus that could be fighter pilots or not, plus the 302 pilots. He had no way of knowing if the list was incomplete, let alone how badly hurt the injured were. The list was completely useless so he used his last resort and armed with his very useless list, he went to see Elizabeth.

"I need your help." Rodney spoke as soon as Elizabeth opened her door, and he entered into her room without waiting for permission. "I need you to promise not to say anything to anyone ever."

"Rodney. Come in, please," Elizabeth admonished the scientist.

"Yeah, yeah, sorry. I'm interrupting your rest, but I need your help."

"Okay. How can I help you, Rodney?"

"You can't tell anyone, ever."

"Okay. I'll keep your secret. Now would you tell me how I can help you so I can go to sleep?" Weir was a little exasperated with Rodney, but if the man was asking for help while looking anxious, it had to be very important.

"I need to find a fighter pilot, American, male who was either in the SGC, the Prometheus or the 302 program during the battle against Anubis. You were in charge of the SGC at the time. Figure he'd know if he had been killed, so he probably was injured, severely." Rodney was rambling in his panic voice.

"I'm confused, Rodney, why are you looking for a pilot? Who is this pilot? What's his name? And who would know what? Please, start from the beginning," Elizabeth calmly tried to get Rodney to focus.

"You're not going to say anything, right?" Elizabeth nodded again. "If you do, he'll hate me."

"Rodney! I promise I won't say anything about whatever this is about to anyone, but please explain what this is about."

"Sheppard was dating someone before coming to Atlantis. He was a pilot assigned to 'testing cool and extremely classified fighter jets' and disappeared from the face of Earth around the time Anubis tried to destroy Earth."

"Who is this guy assigned to what I imagine is the 302 program? What's his name? Was he killed or injured during the battle?"

"I don't know his name. He refused to give it to me. I know he's not dead because he would have been in the list of casualties and then Sheppard would know. Now, if he was injured and unable to contact anyone…"

"Someone would have contacted John, Rodney, like this mysterious pilot's family," Elizabeth argued.

"They didn't know to contact him."

"Okay. So what exactly do you want, Rodney?"

"I need your help to figure out who Sheppard's boyfriend is and what happened to him?"

"Why?"

"Because he thinks the guy hates him, or maybe he doesn't want to accept that he was injured or… I'm not sure exactly how Sheppard's mind works. What I know is that knowing the truth may help him, especially if there were good news."

"This is not about you intruding in his personal life, it is?"

"No, it's not. I promise. I'm worried about him," Rodney answered honestly.

"Okay, then, I'll make a list of candidates and then we'll go over it. Tomorrow. Now, go to bed, and don't say anything to John."

Rodney thanked her and left the room as quickly as he arrived.

* * *

A few nights later, they met again and finally figured out who could be Sheppard's lover thanks to Elizabeth files. The physicist then went looking for the Major in his room hoping to speak with him privately.

"You're probably going to be a bit angry at me, but I hope you forgive me when I tell you the good news."

"Why should I be angry? What have you done?"

"Nothing bad. I just investigated a bit and found your boyfriend. You can thank me later."

"Rodney! Please, tell me you haven't done anything stupid. If anyone finds about this, I'll kill you!" John was white with rage and his voice had turned deadly low and cold.

"I promise your secret is safe. I did nothing to risk that. I swear," Rodney babbled terrified that the Major was actually going to hurt him. "He's alive. He was injured in Antarctica fighting against Anubis and he was taken to the Academy Hospital."

John sat down on the bed, shaking his head. He didn't want to consider this. He had gotten tired of him. He hadn't been injured to the point of not being able to contact him. He didn't even want to consider that option.

"Yes. He's alive. He was in an induced coma for a while, and then dosed up with drugs, but the doctors expected him to recuperate in time. He didn't get tired of you. He's not dead which I know is what you feared the most. He is injured but is going to heal. Hey! He probably is waiting for you to go back to Earth!"

Rodney was rambling so much he hadn't notice that John, who had been deathly still for minutes, was now shaking. "You mean, he's okay?"

"Yeah, John, he is." John nodded and for the first time since McKay entered the room, he smiled honestly.

"Thanks, Rodney. Really."

"You're welcome." Rodney left the room leaving his friend happier than he had been before. He looked relieved like a big weight had been lifted from his shoulders. He had done the right thing finding out about his lover.

* * *

With the Wraith knocking at their door, they prepared a message to send to the SGC which included video messages from the expedition members for family and friends so they could say goodbye.

Elizabeth had done all the death notifications, except for Sumner's, recorded a message for all the families of the living in case the expedition didn't make it, and she still had time for a small message for General O'Neill.

"This message is only for the eyes of General O'Neill and no one is to watch it without his authorization." She was going to trust the General with this particular piece of information, but no one else.

"General, I need to request a favor from you. If we don't survive, every member of my expedition's family will be notified personally. Except for one of them. I'm trusting you to keep this information a secret and do the notification yourself."

"I don't know what your beliefs are, but I do know you would do anything to protect your soldiers, and that you won't deny the request of a dying woman. Would you?" Elizabeth joked at the camera. O'Neill would appreciate the humor.

* * *

After Atlantis was saved, the senior staff of the Expedition with Weir at the head traveled to Earth to report. After surviving a few meetings with the IOA, she decided to have an important conversation with General O'Neill. She knocked at his temporary office in the SGC and waited for the man to let her in.

"Oh, Elizabeth, seeing as you aren't dying, I don't have to follow through with your little request. I think it would have given a certain young pilot a heart attack," O'Neill commented with a smirk.

Elizabeth looked at him, worried that she had put Sheppard's career at risk. "Relax, Doctor, don't go panicking now. I don't care who your military commander is seeing. I think it would have made for an awkward conversation."

Elizabeth smiled at the General. "Good to hear."

"So, what do you want? I don't think you came all the way here to remind me to keep your little secret."

"I didn't. I want to make Atlantis a Colony with enough independence to stop the IOA from…"

"Screwing you over?" Jack smirked.

"Yes. That was my idea. Of course, we can reach an agreement about the laws we should follow, and to coordinate certain operations with you and the SGC…"

"But you want a certain amount of independence," O'Neill finished for her. "If you do that we'll have to negotiate how to deal with the military contingent and the money you get. Let me tell you, the military contingent can be easily arranged in exchange for the advances your people make. And of course, keeping the Wraith away from Earth would get you a lot of bullets."

"What you're saying is that I have your approval and support, right?"

O'Neill laughed softly. "You, Elizabeth, are one damned good negotiator!"

"I'll take that as a yes, General. Though, I don't see any negotiating here, more like you already had a plan."

O'Neill smiled at the diplomat to confirm her suspicions. "You can take it as a yes, as long as the negotiations are done with me and not the IOA. We'll have a fantastic commercial relationship and you'll keep the Wraith very far away from the Milky Way. As long as that's the case, we can make Atlantis a Colony with enough freedom to suit your needs."

"Thank you, General." Elizabeth lingered trying to find a way to get the other thing she wanted from this meeting.

"Something else you wanted, Doctor?"

"Yes. As you know some people are fighting me on making John the Military Commander of the expedition. Apparently he doesn't have the rank."

O'Neill gave her some papers that he retrieved from his desk. "Is this what you want?"

Elizabeth read the papers, happy to see the Sheppard's promotion to Lieutenant Colonel and to Military Commander of Atlantis already approved. She smiled, and her smile grew even more when the General gave her one more piece of paper. "What does this mean?"

"As you know, DADT doesn't apply for the Stargate Program and there's no need for it to apply in your newly minted colony. If, and let me stress the if here, they can be professional and he can follow Sheppard's orders, I'll let him go to Atlantis."

"Thank you, General," Weir said honestly happy with the turn of events. The Expedition will be heading back to Pegasus with enough independence to protect them from the many political interests on Earth but with enough ties to the Stargate Program to get them manpower to fight the Wraith and supplies. She was keeping her team exactly like she wanted and, as the Governor of the colony, she'd get to choose the personnel freely. She was getting everything she wanted as long as O'Neill got the advances they made in Atlantis first, but she trusted O'Neill with that kind of power, she didn't trust the IOA.

"You're welcome. Now, if you don't mind, it seems I have to go visit an unsuspecting airman and give him a heart attack," O'Neill said with a smirk. If he had to go inform one of his soldiers that he knew he was sleeping with another guy and that he could follow that guy to another galaxy if he so desired, then he was at least going to enjoy scaring the guy to hell.

* * *

A few weeks later, the new members of the expedition and the senior staff went back to Atlantis onboard the Daedalus with the new Colony treaties in order, and enough supplies and manpower to continue fighting the Wraith and exploring the Pegasus Galaxy.

The newly minted Lieutenant Colonel Sheppard almost killed McKay and Weir for not being able to keep their mouths shut. They were lucky that O'Neill calmed him down with an honest promise that it would not affect his career and the transfer orders to Atlantis of his partner.

He still wanted to kill his friends, days into their very boring trip to Pegasus aboard the Earth ship. However, going to bed with the man he loved every day kept making the urge to kill them grow smaller every day.

"Baby, go to sleep. You're exhausted from training the newbies. Hell! I'm exhausted from your training." John was holding his lover tightly to him in their bed as if to ensure nothing could come between them.

"Uhm Uhm," John mumbled half asleep and tightened his embrace even more. "I love you."

"I love you too, John, but I need to breathe. I'm not going anywhere, baby. When I told you I wanted to tell my folks about you, it was all to prevent this from happening. I wanted to protect you. I should have explained better instead of getting angry. I'm sorry you thought I had gotten tired of you."

"Don't. Don't apologize. It's not your fault. I got scared and assumed the worst, which actually wasn't the worst. I was so afraid that you had died or gotten terribly injured that I convinced myself that you didn't want me because it was better than the alternative… and…"

His partner kissed him to stop him from rambling anymore. "I know. It's ok. It's over, John. We're together again, on our way to the craziest but most awesome city in two galaxies. Let's enjoy it, eh?"

John smiled brightly and kissed the love of his life with intent.

* * *

 **Icarusancalion:** I hope you like your gift. I wasn't capable of giving you an Independent!Atlantis, but I came close enough. I wanted to give more emphasys to Rodney and John's friendship, and a happy ending. I hope you enjoyed it!

Now, one last thing, this is your gift, so if you want to continue in the road of Independent!Atlantis using this story as the basis for it, then do it. Take us, Gaters, in that fascinating journey.


End file.
